Carbon Source-Dependent Expansion of the Genetic Code in Bacteria
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Regeneration of Unconventional Natural Gas by Methanogens Co
www.nature.com/scientificreports OPEN Regeneration of unconventional natural gas by methanogens co‑existing with sulfate‑reducing prokaryotes in deep shale wells in China Yimeng Zhang1,2,3, Zhisheng Yu1*, Yiming Zhang4 & Hongxun Zhang1 Biogenic methane in shallow shale reservoirs has been proven to contribute to economic recovery of unconventional natural gas. However, whether the microbes inhabiting the deeper shale reservoirs at an average depth of 4.1 km and even co-occurring with sulfate-reducing prokaryote (SRP) have the potential to produce biomethane is still unclear. Stable isotopic technique with culture‑dependent and independent approaches were employed to investigate the microbial and functional diversity related to methanogenic pathways and explore the relationship between SRP and methanogens in the shales in the Sichuan Basin, China. Although stable isotopic ratios of the gas implied a thermogenic origin for methane, the decreased trend of stable carbon and hydrogen isotope value provided clues for increasing microbial activities along with sustained gas production in these wells. These deep shale-gas wells harbored high abundance of methanogens (17.2%) with ability of utilizing various substrates for methanogenesis, which co-existed with SRP (6.7%). All genes required for performing methylotrophic, hydrogenotrophic and acetoclastic methanogenesis were present. Methane production experiments of produced water, with and without additional available substrates for methanogens, further confrmed biomethane production via all three methanogenic pathways. Statistical analysis and incubation tests revealed the partnership between SRP and methanogens under in situ sulfate concentration (~ 9 mg/L). These results suggest that biomethane could be produced with more fexible stimulation strategies for unconventional natural gas recovery even at the higher depths and at the presence of SRP. -
A Three-Component Microbial Consortium from Deep-Sea Salt-Saturated Anoxic Lake Thetis Links Anaerobic Glycine Betaine Degradation with Methanogenesis
Microorganisms 2015, 3, 500-517; doi:10.3390/microorganisms3030500 OPEN ACCESS microorganisms ISSN 2076-2607 www.mdpi.com/journal/microorganisms Article A Three-Component Microbial Consortium from Deep-Sea Salt-Saturated Anoxic Lake Thetis Links Anaerobic Glycine Betaine Degradation with Methanogenesis Violetta La Cono 1, Erika Arcadi 1, Gina La Spada 1, Davide Barreca 2, Giuseppina Laganà 2, Ersilia Bellocco 2, Maurizio Catalfamo 1, Francesco Smedile 1, Enzo Messina 1, Laura Giuliano 1,3 and Michail M. Yakimov 1,* 1 Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina 98122, Italy; E-Mails: [email protected] (V.L.C.); [email protected] (E.A.); [email protected] (G.L.S.); [email protected] (M.C.); [email protected] (F.S.); [email protected] (E.M.); [email protected] (L.G.) 2 Department of Organic and Biological Chemistry, University of Messina, Salita Sperone 31, Villaggio S. Agata, Messina 98166, Italy; E-Mails: [email protected] (D.B.); [email protected] (G.L.); [email protected] (E.B.) 3 Mediterranean Science Commission (CIESM), 16 bd de Suisse, MC 98000, Monaco * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +39-090-6015-437. Academic Editors: Ricardo Amils and Elena González Toril Received: 1 July 2015 / Accepted: 1 September 2015 / Published: 9 September 2015 Abstract: Microbial communities inhabiting the deep-sea salt-saturated anoxic lakes of the Eastern Mediterranean operate under harsh physical-chemical conditions that are incompatible with the lifestyle of common marine microorganisms. -
Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules
Brigham Young University BYU ScholarsArchive Theses and Dissertations 2014-07-01 Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules Ryan M. Taylor Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Biochemistry Commons, and the Chemistry Commons BYU ScholarsArchive Citation Taylor, Ryan M., "Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules" (2014). Theses and Dissertations. 5585. https://scholarsarchive.byu.edu/etd/5585 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules Ryan M. Taylor A dissertation submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Doctor of Philosophy John T. Prince, Chair Mark Clement Steven W. Graves Barry M. Willardson Dixon J. Woodbury Department of Chemistry and Biochemistry Brigham Young University July 2014 Copyright © 2014 Ryan M. Taylor All Rights Reserved ABSTRACT Bioinformatic Solutions to Complex Problems in Mass Spectrometry Based Analysis of Biomolecules Ryan M. Taylor Department of Chemistry and Biochemistry, BYU Doctor of Philosophy Biological research has benefitted greatly from the advent of omic methods. For many biomolecules, mass spectrometry (MS) methods are most widely employed due to the sensitivity which allows low quantities of sample and the speed which allows analysis of complex samples. Improvements in instrument and sample preparation techniques create opportunities for large scale experimentation. -
EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By
EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated -
Supplementary Figure Legends for Rands Et Al. 2019
Supplementary Figure legends for Rands et al. 2019 Figure S1: Display of all 485 prophage genome maps predicted from Gram-Negative Firmicutes. Each horizontal line corresponds to an individual prophage shown to scale and color-coded for annotated phage genes according to the key displayed in the right- side Box. The left vertical Bar indicates the Bacterial host in a colour code. Figure S2: Projection of virome sequences from 183 human stool samples on A. Acidaminococcus intestini RYC-MR95, and B. Veillonella parvula UTDB1-3. The first panel shows the read coverage (Y-axis) across the complete Bacterial genome sequence (X-axis; with bp coordinates). Predicted prophage regions are marked with red triangles and magnified in the suBsequent panels. Virome reads projected outside of prophage prediction are listed in Table S4. Figure S3: The same display of virome sequences projected onto Bacterial genomes as in Figure S2, But for two different Negativicute species: A. Dialister Marseille, and B. Negativicoccus massiliensis. For non-phage peak annotations, see Table S4. Figure S4: Gene flanking analysis for the lysis module from all prophages predicted in all the different Bacterial clades (Table S2), a total of 3,462 prophages. The lysis module is generally located next to the tail module in Firmicute prophages, But adjacent to the packaging (terminase) module in Escherichia phages. 1 Figure S5: Candidate Mu-like prophage in the Negativicute Propionispora vibrioides. Phage-related genes (arrows indicate transcription direction) are coloured and show characteristics of Mu-like genome organization. Figure S6: The genome maps of Negativicute prophages harbouring candidate antiBiotic resistance genes MBL (top three Veillonella prophages) and tet(32) (bottom Selenomonas prophage remnant); excludes the ACI-1 prophage harbouring example characterised previously (Rands et al., 2018). -
Draft Genome Sequence of Dethiobacter Alkaliphilus Strain AHT1T, a Gram-Positive Sulfidogenic Polyextremophile Emily Denise Melton1, Dimitry Y
Melton et al. Standards in Genomic Sciences (2017) 12:57 DOI 10.1186/s40793-017-0268-9 EXTENDED GENOME REPORT Open Access Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile Emily Denise Melton1, Dimitry Y. Sorokin2,3, Lex Overmars1, Alla L. Lapidus4, Manoj Pillay6, Natalia Ivanova5, Tijana Glavina del Rio5, Nikos C. Kyrpides5,6,7, Tanja Woyke5 and Gerard Muyzer1* Abstract Dethiobacter alkaliphilus strain AHT1T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC content, within the phylum Firmicutes. Here we report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1T was sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications. Keywords: Extreme environment, Soda lake, Sediment, Haloalkaliphilic, Gram-positive, Firmicutes Introduction genome of a haloalkaliphilic Gram-positive sulfur dispro- Soda lakes are formed in environments where high rates portionator within the phylum Firmicutes: Dethiobacter of evaporation lead to the accumulation of soluble carbon- alkaliphilus AHT1T. ate salts due to the lack of dissolved divalent cations. Con- sequently, soda lakes are defined by their high salinity and Organism information stable highly alkaline pH conditions, making them dually Classification and features extreme environments. Soda lakes occur throughout the The haloalkaliphilic anaerobe D. alkaliphilus AHT1T American, European, African, Asian and Australian conti- was isolated from hypersaline soda lake sediments in nents and host a wide variety of Archaea and Bacteria, northeastern Mongolia [10]. -
Genome-Scale Analysis of Acetobacterium Bakii Reveals the Cold Adaptation of Psychrotolerant Acetogens by Post-Transcriptional Regulation
Downloaded from rnajournal.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Shin et al. 1 Genome-scale analysis of Acetobacterium bakii reveals the cold adaptation of 2 psychrotolerant acetogens by post-transcriptional regulation 3 4 Jongoh Shin1, Yoseb Song1, Sangrak Jin1, Jung-Kul Lee2, Dong Rip Kim3, Sun Chang Kim1,4, 5 Suhyung Cho1*, and Byung-Kwan Cho1,4* 6 7 1Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of 8 Science and Technology, Daejeon 34141, Republic of Korea 9 2Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea 10 3Department of Mechanical Engineering, Hanyang University, Seoul 04763, Republic of Korea 11 4Intelligent Synthetic Biology Center, Daejeon 34141, Republic of Korea 12 13 *Correspondence and requests for materials should be addressed to S.C. ([email protected]) 14 and B.-K.C. ([email protected]) 15 16 Running title: Cold adaptation of psychrotolerant acetogen 17 18 Keywords: Post-transcriptional regulation, Psychrotolerant acetogen, Acetobacterium bakii, 19 Cold-adaptive acetogenesis 20 1 Downloaded from rnajournal.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Shin et al. 1 ABSTRACT 2 Acetogens synthesize acetyl-CoA via CO2 or CO fixation, producing organic compounds. 3 Despite their ecological and industrial importance, their transcriptional and post-transcriptional 4 regulation has not been systematically studied. With completion of the genome sequence of 5 Acetobacterium bakii (4.28-Mb), we measured changes in the transcriptome of this 6 psychrotolerant acetogen in response to temperature variations under autotrophic and 7 heterotrophic growth conditions. -
A 22Nd Amino Acid Encoded Through a Genetic Code Expansion
Emerging Topics in Life Sciences (2018) https://doi.org/10.1042/ETLS20180094 Review Article Pyrrolysine in archaea: a 22nd amino acid encoded through a genetic code expansion Jean-François Brugère1,2, John F. Atkins3,4, Paul W. O’Toole2 and Guillaume Borrel5 1Université Clermont Auvergne, Clermont-Ferrand F-63000, France; 2School of Microbiology and APC Microbiome Institute, University College Cork, Cork, Ireland; 3School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland; 4Department of Human Genetics, University of Utah, Salt Lake City, UT, U.S.A.; 5Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France Correspondence: Jean-François Brugère ( [email protected]) The 22nd amino acid discovered to be directly encoded, pyrrolysine, is specified by UAG. Until recently, pyrrolysine was only known to be present in archaea from a methanogenic lineage (Methanosarcinales), where it is important in enzymes catalysing anoxic methyla- mines metabolism, and a few anaerobic bacteria. Relatively new discoveries have revealed wider presence in archaea, deepened functional understanding, shown remark- able carbon source-dependent expression of expanded decoding and extended exploit- ation of the pyrrolysine machinery for synthetic code expansion. At the same time, other studies have shown the presence of pyrrolysine-containing archaea in the human gut and this has prompted health considerations. The article reviews our knowledge of this fascinating exception to the ‘standard’ genetic code. Introduction It is now more than half a century ago since the genetic code was deciphered [1,2]. The understanding gained of how just four different nucleobases could specify the 20 universal amino acids to synthesise effective proteins reveals a fundamental feature of extant life. -
Unique Characteristics of the Pyrrolysine System in the 7Th Order
Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette Guillaume Borrel, Nadia Gaci, Pierre Peyret, Paul W. O’Toole, Simonetta Gribaldo, Jean-François Brugère To cite this version: Guillaume Borrel, Nadia Gaci, Pierre Peyret, Paul W. O’Toole, Simonetta Gribaldo, et al.. Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette. Archaea, Hindawi Publishing Corporation, 2014, 2014, pp.1 - 11. 10.1155/2014/374146. hal-01612761 HAL Id: hal-01612761 https://hal.archives-ouvertes.fr/hal-01612761 Submitted on 8 Oct 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Hindawi Publishing Corporation Archaea Volume 2014, Article ID 374146, 11 pages http://dx.doi.org/10.1155/2014/374146 Research Article Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette Guillaume Borrel,1,2 Nadia Gaci,1 Pierre Peyret,1 Paul W. O’Toole,2 Simonetta Gribaldo,3 and Jean-François Brugère1 1 1EA-4678 CIDAM, Clermont Universite,´ Universite´ d’Auvergne, Place Henri Dunant, 63001 Clermont-Ferrand, France 2 Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland 3 Institut Pasteur, Department of Microbiology, UnitedeBiologieMol´ eculaire´ du Gene` chez les Extremophiles,ˆ 28 rue du Dr. -
Microbial Activity in Bentonite Buffers. Literature Study
NOL CH OG E Y T • • R E E C S N E E A I 20 R C C S H • S H N I G O I H S L I I V G • H S T Microbial activity in bentonite buffers Literature study Marjaana Rättö | Merja Itävaara VTT TECHNOLOGY 20 Microbial activity in bentonite buffers Literature study Marjaana Rättö & Merja Itävaara ISBN 978-951-38-7833-7 (URL: http://www.vtt.fi/publications/index.jsp) ISSN 2242-122X (URL: http://www.vtt.fi/publications/index.jsp) Copyright © VTT 2012 JULKAISIJA – UTGIVARE – PUBLISHER VTT PL 1000 (Vuorimiehentie 5, Espoo) 02044 VTT Puh. 020 722 111, faksi 020 722 4374 VTT PB 1000 (Bergsmansvägen 5, Esbo) FI-2044 VTT Tfn +358 20 722 111, telefax +358 20 722 4374 VTT Technical Research Centre of Finland P.O. Box 1000 (Vuorimiehentie 5, Espoo) FI-02044 VTT, Finland Tel. +358 20 722 111, fax + 358 20 722 4374 2 Microbial activity in bentonite buffers Literature study Marjaana Rättö & Merja Itävaara. Espoo 2012. VTT Technology 20. 30 p. Abstract The proposed disposal concept for high-level radioactive wastes involves storing the wastes underground in copper-iron containers embedded in buffer material of compacted bentonite. Hydrogen sulphide production by sulphate-reducing prokar- yotes is a potential mechanism that could cause corrosion of waste containers in repository conditions. The prevailing conditions in compacted bentonite buffer will be harsh. The swelling pressure is 7–8 MPa, the amount of free water is low and the average pore and pore throat di ameters are small. This literature study aims to assess the potential of microbial activity in bentonite buffers. -
MT November 2011
DECEMBER 2011% VOLUME 5, ISSUE 1 The Microbial Taxonomist A Newsletter Published by Bergey’s Manual Trust Fred A. Rainey Elected to Chair of BMT Fred A. Rainey is a native of Join BISMiS or renew your Belfast, Northern Ireland. He membership today! See forms obtained a BSc(Hons) in at end of this newsletter or Microbiology and Microbial join online at: Technology in 1988 from University www.bergeys.org/bismis.html of Warwick. Fred's doctoral studies were carried out at the Thermophile Research Laboratory at the University of Waikato, VOLUME 5 NEWS Hamilton, New Zealand. In 1991 Fred joined the group of Erko Volume 5 of Bergey’s Manual of Stackebrandt at the University of Systematic Bacteriology, which Queensland, Brisbane, Australia. In focuses on the Actinobacteria, is associate and since 2000 as a 1993, when Erko Stackebrandt in the final stages of production. trustee (and secretary). He has became the Director and CEO of contributed many chapters to This volume is the largest of the German Collection of Volumes 1–5 of the 2nd edition of the three that I have managed, Microorganisms and Cell Cultures Bergey's Manual of Systematic and will be more than 2000 (DSMZ), Fred joined the DSMZ Bacteriology and was an Associate pages in length, with 431 figures and set up the molecular Editor of Volume 3, which covered and 320 tables. Its size is such identification laboratory and the Firmicutes. Since his PhD that it will need to be bound in services. studies Fred has been involved in two separate parts. It was at the beginning of 1997 bacterial systematics and has The first round of proofs was that Fred moved to the United authored or coauthored over 200 sent out to the authors in six States and accepted his first papers in the field as well as some batches beginning in August; I academic appointment at 85 book chapters. -
Phylogenomic Analysis Supports the Ancestral Presence of LPS-Outer Membranes in the Firmicutes
Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes. Luisa Cs Antunes, Daniel Poppleton, Andreas Klingl, Alexis Criscuolo, Bruno Dupuy, Céline Brochier-Armanet, Christophe Beloin, Simonetta Gribaldo To cite this version: Luisa Cs Antunes, Daniel Poppleton, Andreas Klingl, Alexis Criscuolo, Bruno Dupuy, et al.. Phy- logenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes.. eLife, eLife Sciences Publication, 2016, 5, pp.e14589. 10.7554/eLife.14589.020. pasteur-01362343 HAL Id: pasteur-01362343 https://hal-pasteur.archives-ouvertes.fr/pasteur-01362343 Submitted on 8 Sep 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License RESEARCH ARTICLE Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes Luisa CS Antunes1†, Daniel Poppleton1†, Andreas Klingl2, Alexis Criscuolo3, Bruno Dupuy4, Ce´ line Brochier-Armanet5, Christophe Beloin6, Simonetta Gribaldo1* 1Unite´ de